Here is the list of the current solutions we adopted or developed at the IBL. The tools are open-source and distributed on GitHub

Jump to:

• Data Architecture

• Visualization

• Video Analysis

• Neural Analysis

Experimental Setup

Paper describing the rig and its use:
The International Brain Laboratory "Standardized and reproducible measurement of decision making in mice", The International Brain Laboratory et al., eLife 2021;10:e63711.

Standardized rig hardware
Appendix 3 from paper (Hardware and Components section)
Rig CAD components
Sourcing hardware from Sanworks

Standardized rig software
Appendix 3 from paper (Software section)
Python Acquisition Software (see also Data architecture publication)
Bpod Firmware

Paper describing the tools used by the IBL: "A modular architecture for organizing, processing and sharing neurophysiology data," The International Brain Laboratory et al., Nat Methods, https://doi.org/10.1038/s41592-022-01742-6

An overview of the code and documentation for all the resources developed or maintained by the IBL can be found on our Welcome Page. Links to information about individual tools can be found there or in the list below.

Alyx

A user-friendly database for neuroscience data and colony management. Click here for the code and installation instructions; click here for documentation on usage.

MTSComp

A lossless compression scheme for electrophysiological data. Click here for the code and usage instructions.

ONE

The Open Neurophysiology Environment (ONE) is data-sharing standard for neurophysiology that can be used by individual labs and large or small collaborations. For information on how to share data with ONE, please click here.

This GitHub page contains an API for searching and loading ONE-standardized data, stored either on a user’s local machine or on a remote server. Click here for the code; click here for usage documentation on using the ONE API; click here for detailed descriptions of IBL datasets and here for a spreadsheet of the latest dataset types.

brainbox

A python library of independent analysis functions oriented towards behavior and neurophysiology. Click here for the code; click here for the documentation.

Datoviz

A generic interactive data visualization library leveraging the graphics processing unit for high rendering performance. Click here for the code and installation instructions.

iblenv

A unified environment and issue tracker for all IBL Github repositories. Click here for the repository and setup instructions.

ELECTROPHYSIOLOGY ALIGNMENT GUI

A desktop tool to align histology tracks using electrophysiology features. Click here for the documentation.

atlas.internationalbrainlab.org

A website that allows data collected across the brain to be explored in an interactive manner using multiple different brain projections. View the website here. Click here for documentation and how to upload your data to the website. Click here for the bioRxiv paper.

PINPOINT

A web-based trajectory planning tool. View the website here. Click here for documentation.

URCHIN

A Python package for rendering data in its original 3D anatomical context. Click here for documentation

Lightning Pose

A cloud-native open-source tool for animal pose estimation via semi-supervised learning and Bayesian ensembling

Click here for code and documentation

Click here for a series of video tutorials

Click here for the Nature Methods paper

IBL-sorter

A spike sorting pipeline built to analyze data from large silicon probe electrode arrays at scale.

Click here for code and documentation

Click here for the paper